The Muslim Brotherhood has fired a warning shot at Egypt's ruling generals, declaring that a swift end to military rule is the country's "top priority" as it prepares to take charge of a newly elected parliament.

With provisional election results continuing to emerge, confirming earlier predictions of a strong victory for the Brotherhood's Freedom and Justice party, the movement's leaders emphasised that now was the time for "consensus not collision" and agreed to work with parties across the political spectrum to advance the revolution and facilitate a smooth transition to civilian government.

In a sign the Brotherhood will not tolerate parliament being treated as a rubber stamp by the Supreme Council of the Armed Forces (Scaf), which has clung to power despite almost two weeks of anti-junta protests and violent street clashes, senior members of the organisation told the Guardian the generals risked further unrest if they defied the people and failed to return to their barracks next year.

"Egypt is currently going through a critical era in its history, and I am confident the military will choose to cooperate with parliament and not confront it – any other path will create more chaos," said Essam al-Arian, vice president of the Freedom and Justice Party.

Amr Darrag, the group's chief in Giza, said a quick and painless handover to civilian rule was the most important issue facing the Arab world's most populous nation at present. "We are going through a transitional phase and we are not yet at the optimum stage of this transition," he argued. "Parliament must be formed, a president must be elected, and power must be transferred to civilian authority. Scaf currently wields executive and legislative power; as soon as parliament convenes the latter must be passed to the institution democratically elected by the Egyptian people."

The comments reveal a shift in rhetoric by the Brotherhood, which has faced heavy criticism by revolutionaries in recent days for refusing to back demonstrations against Scaf which were attacked by security forces, leaving more than 40 dead and thousands injured.

Apparently acknowledging the shifting political sands, Egypt's ruling generals announced on Thursday they would be convening a civilian advisory council to assist Scaf in administering the country during a volatile period.

Officials suggested the council would act as a buffer between protesters and the armed forces and would consist of thirty members, with eight seats allocated to representatives of the 'revolutionary youth'.

But Scaf's credibility has been eroded since it assumed power from Hosni Mubarak in February, as political figureheads – including presidential contenders Abdel Munim, Aboul Fotouh and Hamdeen Sabahi – denounced the proposal and declared they would not be part of it.

"Those who met with the military [to discuss the council] only represent themselves; they are only providing Scaf with a fig-leaf to help it absorb popular anger," Khaled Tellima, a member of the Revolutionary Youth Coalition, told local news outlet Ahram Online. "Our demands are clear: we don't want advisers for the military rulers, we simply want the military rulers to go."

Mamdouh Hamza, a political activist and prominent engineer, claimed he had been offered a place on the new council but had turned it down. Official election results from the first round of voting, which included Egypt's two biggest cities, Cairo and Alexandria, have been pushed back to Friday evening after officials claimed counting was taking longer than expected.

The announcement of results is set to coincide with another anti-Scaf demonstration, after revolutionary forces said they would rally in Tahrir Square to honour the ''martyrs of Mohamed Mahmoud Street" – a reference to the road where fighting took place last week.